The best books that can be referred to, for JEE Mains and Advanced for preparation in Physics, Chemistry and Mathematics.
Physics:
• Concepts of Physics Vol. 1 : http://amzn.to/2tqQzQU
• Concepts of Physics Vol. 2 : http://amzn.to/2ssRlZj 
• Mechanics Part-1 by DC Pandey : http://amzn.to/2uqg8hQ
• Mechanics Part-2 by DC Pandey : http://amzn.to/2tstTzc
• Understanding Physics Electricity and Magnetism by DC Pandey : http://amzn.to/2upXN4B
• Understanding Physics for JEE Main & Advanced Optics & Modern Physics by DC Pandey : http://amzn.to/2t7wtsk
• Understanding Physics for JEE Main & Advanced Waves & Thermodynamics by DC Pandey : http://amzn.to/2sXKwCs
• New pattern Physics Book by DC Pandey - a great book for problems! : http://amzn.to/2tqVwt9
Chemistry :
• New Pattern Textbook of Physical Chemistry for Competitions (JEE Main & Advanced ) by OP Tondon : http://amzn.to/2t7iRNS
• Modern Approach to Chemical Calculations by RC Mukherjee : http://amzn.to/2s89VGw
• Numerical Chemistry 22/e by P Bahadur : http://amzn.to/2ts9rPe
• Organic Chemistry by LG Wade : http://amzn.to/2ssKbnU this is the BEST possible book for organic chemistry. DON'T buy OP Tondon organic chemistry. Many aspirants buy random books and then the book says something in 1 chapter and something contradicting in the other chapter. If you trust me, buy this book and see the magic of organic chemistry. 
• Organic Chemistry by Morrison Boyd : http://amzn.to/2tst3m5 you must read this book once if you are appearing for JEE. This is the so called "HC Verma" of organic chemistry
• Textbook of Inorganic Chemistry for Competiotions (JEE Main & Advanced ) by OP Tondon : http://amzn.to/2u5ptwc
Mathematics
• RD Sharma class 11th and RD Sharma class 12th : http://amzn.to/2u5uq87 people tend to underestimate the school level books. But these are the ones that will build your foundation.
• Coordinate Geometry for IIT-JEE by SK Goyal : http://amzn.to/2staxpJ indeed a great book for Coordinate geometry. Its subjective problems are excellent
• Differential Calculus for IIT-JEE by Amit Agarwal : http://amzn.to/2sXAj8R
• Integral Calculus for IIT-JEE by Amit Agarwal : http://amzn.to/2sXnlIg
• Vectors & 3D Geometry by Arihant Publications : http://amzn.to/2stfMFX
• Trigonometry for JEE Main & Advanced by Arihant Publications : http://amzn.to/2u5sfSd
• COURSE in MATHEMATICS for IIT-JEE (TMH) : http://amzn.to/2s8v7w6 I would say that this is the best book for JEE when it comes to problems. The algebra section is the best in this book
• A Practice Book of Mathematics JEE Main & Advanced by Arihant Publication : http://amzn.to/2s7R4f2\
Additionally, to complete your preparation, you must solve the past year JEE papers:
• 38 Years' Chapter-wise Solved Papers (2016-1979) IIT JEE Physics : http://amzn.to/2s8hOf3
• IIT JEE - Mathematics : 38 Year's Chapter-wise Solved Papers (2016 - 1979) : http://amzn.to/2stgPpf
• IIT JEE - Chemistry : 38 Year's Chapter-wise Solved Papers (2016 - 1979) : http://amzn.to/2snfCov
Besides, if you are looking for general preparation guidance, you can have a look at the following:
• The Secret of My Success Book : http://amzn.to/2st4QrJ